TMCC3

transmembrane and coiled-coil domain family 3, the group of MicroRNA protein coding host genes|Transmembrane and coiled-coil domain containing

Basic information

Region (hg38): 12:94567122-94650557

Links

ENSG00000057704NCBI:57458OMIM:617459HGNC:29199Uniprot:Q9ULS5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMCC3 gene.

  • not_specified (67 variants)
  • not_provided (3 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCC3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020698.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
3
missense
66
clinvar
1
clinvar
67
nonsense
2
clinvar
2
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 68 2 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TMCC3protein_codingprotein_codingENST00000261226 483439
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00002740.9341257120351257470.000139
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9232312740.8430.00001633113
Missense in Polyphen102135.490.752841592
Synonymous0.3021131170.9650.00000783914
Loss of Function1.701017.70.5640.00000105207

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002700.000268
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.0001590.000158
Middle Eastern0.00005440.0000544
South Asian0.0002290.000229
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.110

Intolerance Scores

loftool
0.785
rvis_EVS
0.18
rvis_percentile_EVS
66.13

Haploinsufficiency Scores

pHI
0.0962
hipred
N
hipred_score
0.204
ghis
0.458

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.163

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tmcc3
Phenotype

Gene ontology

Biological process
Cellular component
integral component of membrane
Molecular function
protein binding